Employees of the Washington Navy Yard line up to enter through a gate on Sept. 18, two days after a gunman killed twelve people and was killed himself inside. (Jacquelyn Martin / AP)

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WASHINGTON — The decision to grant a security clearance to a government contractor who later killed 12 people at the Washington Navy Yard was made without a review of a critical police report, but background investigators still followed the correct standards, the top federal personnel management official told a Senate panel Thursday.

The Senate committee on Homeland Security and Governmental Affairs is investigating the nation’s security clearance system in the aftermath of the Sept. 16 shooting involving Aaron Alexis, a former Navy reservist and IT contractor. He was awarded, and held onto, a secret clearance despite brushes with law enforcement, a series of angry outbursts and concerns about his mental health that led Rhode Island police to his hotel room just one month before the shooting.

Elaine Kaplan, acting director of the Office of Personnel Management, said background investigators who vetted Alexis did “what they were supposed to do,” but acknowledged they lacked a complete portrait of his past. She said Alexis was approved for the clearance even though investigators never reviewed a 2004 police report from Seattle that accused him of shooting out the tires of an unoccupied vehicle, relying instead on court records that did not reveal the circumstances of the arrest.

Though the contractor that handled the background check followed the investigative standards, Kaplan said current expectations may not be stringent enough.

“Are the standards up to snuff? Should we be required to get police reports, for example? Should we be required to get mental health information, even for someone who has a secret as opposed to a top secret clearance? All these things need to be looked at,” Kaplan said. “But it was not, in our view, a case of malfeasance on the part of the contractor.”

President Obama has also ordered the White House budget office to examine security standards for government contractors and employees across federal agencies. Concerns about weaknesses in the security clearance system have surfaced not only with Alexis but with National Security Agency leaker Edward Snowden and with Army Pvt. Chelsea Manning, currently imprisoned for leaking classified documents.

Alexis was granted a secret clearance in 2008 and held onto it despite multiple subsequent encounters with police, including a 2010 arrest in Texas, where a neighbor told police she was nearly struck by a bullet fired from his downstairs apartment. No charges were filed.

One month before the Navy Yard shooting, Alexis called police in Rhode Island to the hotel where he was staying and complained about voices wanting to harm him, according to the police report. After the shooting, the FBI said writings recovered in Alexis’s possession showed he believed he was being bombarded with extremely low frequency radio waves.

Federal officials said they were working to retool aspects of the nation’s security clearance system, including the process of re-evaluating the behavior of employees and contractors who have access to sensitive information. Holders of top secret clearances are re-investigated every five years and those with secret clearances every 10 years.

One change being pursued is to allow that review to happen any time, including automated checks of government and commercial databases, said Brian Prioletti, an assistant director in the Office of the Director of National Intelligence.

Alexis applied for a security clearance with the Navy in 2007. Defense officials say he lied in his application about a 2004 arrest in Seattle for shooting the tires of an unoccupied vehicle and he failed to disclose thousands of dollars in debts. An FBI fingerprint check revealed the arrest, but an investigative report from an OPM contractor omitted the fact that Alexis had fired shots and court records in Seattle did not reveal details on the arrest and showed only that malicious mischief charges were not pursued.

She said investigators were not required to review the underlying police report and did not even try to access it because the Seattle police department, like other jurisdictions, had a history of not making such information available to contractors doing background checks. She acknowledged that it was “problematic, certainly, that there’s information written on a piece of paper somewhere that we didn’t have access to.”

Sen. Kelly Ayotte, a New Hampshire Republican, said it was “incredibly shocking” that investigators did not make an effort to access the report.

“A prosecutor may not have the elements to make a particular charge and the disposition may tell us nothing. But seeing a prior behavior here with Aaron Alexis, getting a police report, would have flagged a very different set of conduct for anyone looking at that,” Ayotte said.

Senators on the committee said they were concerned that too much information was classified and too many employees and contractors have security clearances.

“Many national security experts have long argued that the security clearance process is antiquated and in need of modernization. Given recent events, I think we have to ask whether the system is fundamentally flawed,” Sen. Tom Carper, a Delaware Democrat and committee chairman, said in his remarks.

Four senators have introduced legislation to require more frequent checks on government employees and contractors who are awarded security clearances.

The bill requires OPM to do at least two audits of every security clearance at random times over each five years the clearance is in effect. Surprise audits would send the message that “you never know when the government is going to find out,” so it’s better to come forward with the information voluntarily, said one sponsor, Democratic Sen. Claire McCaskill of Missouri.